Satellite imagery of the blue-green waters of the Chesapeake Bay on Sept. 13 from NASA’s Rapid Response: (NASA/GSFC, Rapid Response/NASA/GSFC, RAPID RESPONSE)

Late Tuesday morning, John Page Williams set out on a tour of some sights that no one in his boat really wanted to see: the blue-green waters of the Chesapeake Bay turned brown by storm water runoff and sewer overflows caused by downpours from Tropical Storm Lee.

“It was just chocolate,” said Williams, a senior naturalist for the Chesapeake Bay Foundation. During his three-hour tour, he encountered huge tree limbs, plastic foam, a yoga mat and what looked like “somebody’s firewood from a wood pile.” A sediment-laden brown streak covers nearly half of the the 200-mile-long bay. “It’s a mess,” Williams said.

Williams encountered scientists from the National Oceanic and Atmospheric Administration, the U.S. Geological Survey, the University of Maryland and the Maryland Department of Natural Resources as he sailed 400 yards from a section of the Chesapeake Bay Bridge in his 17-foot Boston Whaler. The agencies were measuring the flows, sediment and pollution.

Drenching rains from remnants of Lee produced the second-largest water flows from the Susquehanna River into the bay since Hurricane Agnes in June 1972. Flows from Agnes were measured at more than 1 million cubic feet per second. A major snow melt in 1996 caused a flow of more than 900,000 cubic feet per second. The peak flow from Lee was more than 750,000 cubic feet per second.

The flows constituted an expressway for pollution. They were so heavy, said Mark Trice, a research statistician for the Natural Resources Department’s Tidewater Ecosystem Assessment Division, that every gate of the Conowingo Dam in northeastern Maryland was flung open. Sediment and junk that had collected behind the dam for years was released into the Susquehanna.

On top of that, more than 500 million gallons of diluted sewage washed into bay waters in Maryland alone during recent storms. An estimated 200 million gallons poured in from the District.

In addition, runoff from farms washed in livestock manure and fertilizer containing nitrogen and phosphorous, and the flow from city and suburban streets, lawns and rooftops contributed more nitrogen and phosphorous, as well as garbage.

This is the kind of pollution cocktail that created this summer’s Chesapeake Bay “dead zone,” one of the largest on record. Dead zones — caused by pollution-fed algae blooms — come every summer and generally end in the early weeks of fall. This year, Hurricane Irene blew the dead zone to smithereens before its time.

But now, marine biologists are worried that sediment and other pollution that Lee washed into the water will give rise to a secondary dead zone. In a dead zone, the lack of oxygen in the water kills marine species that cannot move out of the way, including oysters and mollusks that use oyster shells as a habitat.

Bay oyster populations in Maryland, and probably Virginia, are so imperiled that a recent study called on state officials to call a halt to the oyster harvest. And even that, the study’s author said, might not save the oysters.

If the pollution spill does not create a secondary dead zone this year, it might increase the size of next summer’s, Williams said.

If there’s a silver lining in the current situation, it is that Lee struck in September. Agnes, by comparison, arrived in June and dumped tons of silt on underwater grasses in the Susquehanna flats that had not begun to seed. Those grasses, which serve as the largest breeding ground for striped bass in the Atlantic Ocean, and perhaps the world, were snuffed out. In June, the fish are too small to survive without them.

“Put yourself in the position of a fish,” Trice said, commenting on bay pollution. “If a similar thing happened on land, and it was air pollution, it would stress you out. You wouldn’t be happy that your environment is changing rapidly.”

Water volume is not a problem, he said: Fish go with the flow. Human pollution is the problem.

“This is us. This is every thing from everybody who eats food and drives around in a car,” Williams said after ending his boat tour. “It’s got all kinds of stuff in it. You don’t want to swim in it. Truth is, you don’t want to run a boat in it unless you really need to.”